RetrogeneDB ID: retro_ocun_1283

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 6:19153535..19154745(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000024012
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MINPP1
• Ensembl ID: ENSOCUG00000002908
• Aliases: None
• Description: multiple inositol-polyphosphate phosphatase 1 [Source:HGNC Symbol;Acc:7102]

Sequence

>retro_ocun_1283
AAAATGGGGGCTGCCGTAGCACCTGCCGTGGCCCTGGCTGCGGCGTTGCTCTCATCTCTCATGTGCTGCTCCCTCCTGGG
GCCCAGTGACCCAGTGGCCTCGGTGTTGAGCCCCTACTTTGGCACCAAGACTCGCTACGAGGATGTCAACCCCAGGCTGG
TTTTGGACCCCGAGGTGCACCTGCACCCCGGTGCAGCTGGTCGCCCTCATCCGCCATGGCACCCGCTACCCCACGGCTAA
ACAGATACGCAAGCTGAGGCAGCTGCACGGGCTGCTGCAGGCCCGCGGCCGCAGCAGTGCGGGCGGTCGCCACCTGGGCG
CGGCGCTGGCCGATTGGCCCCTGGGGTACGCCGACTGGATGGACGGGCAGCTGGTGGAAAAGGGACGGCAGGACATGCGA
CAGCTGGCGCTACGCCTGGCATCGCTGTTCCCGGCCCTCTTCAGCCGGGAGAACTACGGCCGCCTCCGTCTCCTCACCAG
CTCCAAGCACCGCTGCGTGGACAGCGGCGCCGCCTTCCTGCAGGGGCTGTGGCAGCACTACCACCCTGGGTTGCCGCCGC
CGGACGTCGCAGATACGGAGTGTGGACCTCCAAGGATTAATGATAAATTGATGAGATTCTTTGATCATTGTGAGAAGTTT
TTAACTGAAATGGGAAGGAATGCTACGGCTCTTTATCACGTAGAAGCCTTCAAAACTGGACCAGAAATGCAGAACATTTT
AAAGAAAGTTGCAGCTACTTTGCAAGTGCCAGTAAATGATTTAAATGCAGATTTAATTCAGGTAGCTTTTTTTACCTGTT
CATTTGACCTGGCAATTAAAGGTGTTAAGTCTCCTTGGTGTGATGTTTTTGACATAGATGATACAAAGGTATTAGAATAT
TTAAATGACCTGAAACAGTACTGGAAAAGAGGACATGGCTATACTATTAATAGTCGATCCAGTTGCACCTTGTTTCAGGA
TATCTTCCAGCACTTAGACAAAGCAGTTGAACAGAAGCAAAGATCTCAACCGATTTCTTCTCCAGTCATTCTCCAGTTTA
GTCATGCAGAGACCCTTCTACCACTGCTTTCTCTCATGGGCTACTTCAAAGACAAGGAGCCCCTGACAGCTTATAATTAT
AAGGAACAAATGCACCGGAAGTTCCGAAGTGGTCACATTGTACCTTATGCCTCAAACCTGATATTTGTGTTTTACCATTG
TGAGGACGCT

Alignment

ORF - retro_ocun_1283 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.56 %
• Parental protein coverage: 85.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RLGAAVAPAVALAG-MLSSLVCCSLLGPSDPVASVLSPYFGTKTRYEDVNPRLVLDPEV-TCTPVQLVAL
          ..GAAVAPAVALA...LSSL.CCSLLGPSDPVASVLSPYFGTKTRYEDVNPRLVLDPEV.TCTPVQLVAL
Retrocopy KMGAAVAPAVALAAALLSSLMCCSLLGPSDPVASVLSPYFGTKTRYEDVNPRLVLDPEV>TCTPVQLVAL

Parental  IRHGTRYPTAKQIRKLRQLHGLLQARGRGSAGGRDLGAALADWPLGYADWMDGQLVEKGRQDMRQLALRL
          IRHGTRYPTAKQIRKLRQLHGLLQARGR.SAGGR.LGAALADWPLGYADWMDGQLVEKGRQDMRQLALRL
Retrocopy IRHGTRYPTAKQIRKLRQLHGLLQARGRSSAGGRHLGAALADWPLGYADWMDGQLVEKGRQDMRQLALRL

Parental  ASLFPALFSRENYGRLRLLTSSKHRCVDSGAAFLQGLWQHYHPGLPPPDVADMECGPPRINDKLMRFFDH
          ASLFPALFSRENYGRLRLLTSSKHRCVDSGAAFLQGLWQHYHPGLPPPDVAD.ECGPPRINDKLMRFFDH
Retrocopy ASLFPALFSRENYGRLRLLTSSKHRCVDSGAAFLQGLWQHYHPGLPPPDVADTECGPPRINDKLMRFFDH

Parental  CEKFLTEVERNATALYHVEAFKTGPEMQNILKKVAATLQVPVNDLNADLIQVAFFTCSFDLAIKGVKSPW
          CEKFLTE..RNATALYHVEAFKTGPEMQNILKKVAATLQVPVNDLNADLIQVAFFTCSFDLAIKGVKSPW
Retrocopy CEKFLTEMGRNATALYHVEAFKTGPEMQNILKKVAATLQVPVNDLNADLIQVAFFTCSFDLAIKGVKSPW

Parental  CDVFDIDDARVLEYLNDLKQYWKRGHGYTINSRSSCTLFQDIFQHLDKAVEQKQRRSQPISSPVILQFGH
          CDVFDIDD..VLEYLNDLKQYWKRGHGYTINSRSSCTLFQDIFQHLDKAVEQKQ.RSQPISSPVILQF.H
Retrocopy CDVFDIDDTKVLEYLNDLKQYWKRGHGYTINSRSSCTLFQDIFQHLDKAVEQKQ-RSQPISSPVILQFSH

Parental  AETLLPLLSLMGYFKDKEPLTAYNYKEQMHRKFRSGHIVPYASNLIFVLYHCENA
          AETLLPLLSLMGYFKDKEPLTAYNYKEQMHRKFRSGHIVPYASNLIFV.YHCE.A
Retrocopy AETLLPLLSLMGYFKDKEPLTAYNYKEQMHRKFRSGHIVPYASNLIFVFYHCEDA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.99 RPM	21.69 RPM
SRP017611_kidney	1.62 RPM	19.66 RPM
SRP017611_liver	0.39 RPM	6.94 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1283 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1283 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1283 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013275	4 retrocopies	retro_chof_1750, retro_chof_387, retro_chof_786, retro_chof_796,
Mus musculus	ENSMUSG00000024896	1 retrocopy	retro_mmus_2502,
Oryctolagus cuniculus	ENSOCUG00000002908	1 retrocopy	retro_ocun_1283 ,
Rattus norvegicus	ENSRNOG00000011287	1 retrocopy	retro_rnor_32,